SGA's Continuum
by Chris7221
Summary: The Atlantis crew finds themselves in a very different reality. Set in, and spoilers for, Stargate Continuum. ABANDONED
1. Rising Again

Title: SGA's Continuum

Description: Somewhat of an AU. When Ba'al rewrites history, SGA-1 finds Atlantis completely empty.

Occurs: Late Season 3

Spoilers: Stargate Continuum, possible Atlantis Season 3

* * *

'Go, go go! Everyone back to the gate!" yelled Sheppard over the gunfire. He fired his P90 at their pursuers, who promptly fired back.

"I thought this was supposed to be a diplomatic mission!" yelled Dr. Weir, running ahead to dial the gate.

"As did I. However things do not always turn out as they should."

"What the hell-" yelled Sheppard. "Did that guy just- disappear?"

"One less for us to take down." grunted Ronon.

"Whatever, get through the gate!" yelled Sheppard, punching in his iris code while draining the last of his ammo.

* * *

"Engage the shield!" Sheppard yelled, his voice echoing. "Hello?" He looked around and found the gate room empty. "Teyla, Ronon, cover the gate!" Sheppard ran through the gateroom door and up a staircase to the control room. He slammed down his fist on what he hoped was the shield control. The dialing computer buzzed and the button lit up. Before he could hit what he hoped was actually the shield button the gate disengaged, with no one coming through.

"What the hell is going on?" asked Dr. Weir. The rest of ATL-1 and Dr. Beckett was in tow.

"I don't know, it doesn't make sense! The control room is empty!" squawked Rodney from behind a console.

"Rodney," warned Sheppard. "Maybe some sort of radiation attack?"

"No, it couldn't have been a hurried evac," Rodney paused. "Oh no. This is bad."

"Rodney." This time it was Dr. Weir. "What's the problem."

"The whole city is empty, the ZedPM is almost depleted, an we're submerged. It's just like when we got here the first time. Oh yes and hold on, because we're about to rise."

There was a rumble as the clamps released from the ocean floor then a steady vibration as the city began to rise. Soon the city surfaced with a massive splash of water.

A lost city had risen again.

But didn't it do that just a few years ago?

"Colonel, I want you to check for any signs of our people," ordered Dr. Weir. "Rodney, try to figure out what happened."

Rodney was already unpacking his tablet. "What- oh yes, that's what I was doing."

* * *

"There's no one and nothing. The lights are on, but nobody's home." reported Sheppard.

"We don't have any food or medical supplies either." reported Carson.

"The computer is like no one touched it for thousands of years. There's no record of us or anyone else being here before. It's like the last few years have been undone. That includes the ZedPM."

"Well one thing's for certain. We have to contact Earth soon, or we won't be able to survive." Sheppard chimed in.

"Dagan." said McKay.

"We force it out of them?" asked Sheppard.

"Are you sure that's wise?" asked Dr. Weir.

"Would you rather take one from Asuras?" asked McKay.

"Well, it would be more ethical," commented Weir.

"Forget it, we need that ZPM!" stated Sheppard.

"He's right, you know. We need that ZPM, and we need it quick."

"Okay, I'll allow it. Rodney, you stay here with me and Dr. Beckett." Elizabeth sighed. It was her only choice.

The next chapter will be longer. Please leave a review. They help me a lot.


	2. Dagan ZPM

This chapter is a little longer. Still not much thoughts and emotions. Don't worry, they will come in the next chapter. Promise.

As soon as Sheppard stepped through the gate he knew something was wrong. The smoking crater where the villiage used to be confirmed that. _Oh shit. So much for this planet._

"The Wraith were here."

"No, this wasn't the Wraith," stated Ronon.

"Not the damn Genii," replied Sheppard. "Oh shit. The nuke! Decontam, everyone!" At his order everyone pulled on gas masks and gloves. "I don't think it's that much radiation, it looks like it went off a while ago." That calmed everyone's nerves slightly.

"Let's get this done quick everybody. Spread out and look for the ZPM."

Teyla immediately found something. "I have found something. I believe it is a map to the ZPM."

Sheppard took a look. "Isn't this the same map we used a few years ago? Well, it might be worth a look. Move out!"

* * *

Soon they had located the position on the map. There was already a hole dug and the same secret chamber they were in before was revealed. Sheppard climbed inside first and was greeted to a grusome sight. "There's a bunch of dead bodies in here- I don't think you want to come in!" He was glad he couldn't smell anything through the mask. "Ok, look for the ZPM." He opened a chest and found only rotten food. He found a sack near the ZPM release controller but only found a Genii pistol inside.

"Yup, it was our buddies the Genii all right." Sheppard held up the pistol for the others to see. As he did he noticed something. All nine tiles were on the control platform but not in the right order. "I think they put the ZPM back," he told the rest of his team, "I'm gonna try to get it out."

"Be careful," said Teyla, remembering last time they had tried to retrieve the Potentia.

Sheppard arranged the tiles into the magic 15 grid and slid his gloved hands onto their spots. Surprisingly, it worked and the ZPM popped out of the wall.

"Back to the gate we go!"

* * *

"You're clean," stated McKay, putting down his scanner. "Let me remind you that if the bomb had just gone off, you'd all be dead by now. Next time get me to scan it before you go on a ZPM hunt." McKay's temper was only dampened by the fact that they had a ZPM. "Now, give me that ZPM so I can install it.

Sheppard handed over the ZPM. "Don't drop it." McKay gave him a funny look as he hurried out of the control room.

A few minutes later he was back. "We should have power now," he went to a console where his tablet was set up. "And we do."

Dr. Weir finally spoke. "Dial Earth."

McKay walked over to the DHD and started dialling. The DHD buzzed and the Stargate lit up and made noise in response. The unstable vortex ejected to reveal a mesmerizing puddle of water in the center.

Sheppard picked up his radio. "Stargate Command, this is the Atlantis Expedition, please respond.

* * *

_What the hell, that sounds like Sheppard!_ thought Colonel Johnson, the officer on duty at the other end.

"This is Colonel Johnson of Earth. Please identify yourself."

"This is Lieutenant Colonel Sheppard of the Atlantis Expedition. Can I talk to General Landry."

"Negative. I happen to have the real Sheppard over here. Who are you for real?"

"I already told you!" Johnson thought he heard someone yell, "Rodney, what the hell is going on!"

* * *

"Oh no. I think I figured out what happened," said McKay. "And it's not good."

"Tell me," said Sheppard menacingly.

"We're in an alternate reality. It's the only thing that makes sense! Why would there be a Colonel Sheppard on the other end? What happened to Dagan? At first I thought we went back in time but I checked the Ancient clock and Dagan was..." He stopped. "Well at least we have _our _ZPM."

"I don't like the way you said that," said Sheppard. Dr. Weir had taken over the radio.

"What I'm saying is that Earth probably has no ZPM. They might not even have a ship. We can go back to Earth, but we won't be able to come back."

Soon after McKay finished his sentence the gate disengaged.

"How'd it go?" Sheppard asked.

"They're waiting for SG-1 to arrive. Apparently they also made it to this reality."

"Do they have a ZPM?"

McKay got the answer he was expecting. "No."

"How long can we stay here?" asked Dr. Weir.

"A day, maybe longer if we conserve."

How will the team deal with the decision they have to make? Find out next time on Stargate Atlantis!

Ok that was a bad reference, sorry.


	3. Proclarush Taonas

Once I started this chapter it just flew out of my hands. Not a lot of Atlantis, more SG-1 in this chapter. Sorry!

"Atlantis is calling home."

The airplane ride was not a pleasant one for SG-1. Along the way they were constantly interrogated about Atlantis.

"They must have got here the same way we did," replied Sam.

"And how are we supposed to respond? Weir said it herself, we need a what did you call it, 'zero point module'."

"I've told you already, we need to go to Proclarush Taonas," Daniel wasn't handling the interview any better than Sam.

"And how do you plan to get there? We don't even know the address!"

"I'm telling you, I don't know. Ask Sam or even Daniel,"

"We've stolen a cargo ship before! I thought the whole point was to get Atlantis!" retorted Sam angrily.

"We don't need a cargo ship. We get Atlantis to send a Jumper, and then we can fly from a nearby planet."

"Daniel's right. We just need a jumper."

By the time the plane landed SG-1 was tired, seriously annoyed, and equipped with a complete plan.

* * *

"Ah, you're just in time! Atlantis is due to check in in 5 minutes, which gives me some time to talk to you," said General Landry. "We want the ZPM as much as you do, although for a different reason. Let's just say we're interested in the tecnology in Atlantis."

"I'll let you go on this mission, but Colonel O'Neill and a squad of five is going with you."

"We needed him anyway, sir,"

"Scheduled offworld activation!" someone yelled over the intercom.

"Ah, it's about time." Landry led SG-1 to the control room.

"Sheppard, this is Mitchell,"

"What? Wait, SG-1 Mitchell or Mitchell from this reality?"

Carter piped up this time, "We were in transit when the timeline shifted. That's how we got here."

McKay's voice came through the speaker, "That makes sense, I think that's how we got here too. I mean, I figured it out first of course."

"We've got a plan to get a ZPM, but we need your help," stated Daniel. "You see, we need a Jumper."

"What? I mean how are we supposed to give them a Jumper? You can't just push them-"

"Relax, McKay, I'll take one through. And you can have my rations."

Sheppard spoke into the speaker this time. "Do you mind opening the iris to let me through?"

"Open the iris," ordered Landry. Five minutes later the jumper came through.

"All right folks, you have an hour to pack what you need and put it in that... thing of yours," ordered O'Neill. Looking through the hatch of the jumper, he thought he saw the console wiggle. He shook it off. "Trick of the light." What he saw was actually the DHD of the Jumper changing into Milky Way form. It still lit up blue but three more buttons popped out of hidden covers and the symbols changed into the constellations of the Milky Way. Sheppard was surprised, but not as much. _Stranger things have happened._

* * *

An hour later the entire team was assembled and ready. The Jumper was quite full with ten people and a lot of equipment.

"Dial the gate," ordered O'Neill over his radio.

"No need, sir," said Sheppard. He was sitting in the front with Mitchell. He pressed the DHD keys in rapid succession. The gate spun and lit up to the buzzing of the DHD. Finally, the seventh chevron locked and the gate activated, the unstable vortex missing the Jumper by mere inches. The Jumper lifted off and sped through the gate.

"This will be a bit of a long ride," said Sheppard. "It'll take about two hours to reach Taonas."

"Anyone want an airline meal? No? No one wants one?" asked O'Neill in his usual humourous fashion.

Carter smiled. O'Neill was the same in this reality.

"How do you fly this thing, anyway?" asked O'Neill.

"With your mind."

"Sounds creepy."

"Not really. Wanna try."

"No thanks, I'd rather not have my brain sucked out,"

Sheppard, Mitchell, Sam, and Daniel all burst out laughing.

"What? Is it something I said?"

"Nevermind, sir."

* * *

"Okay, we need to find a dome of solidified rock, that's what Taonas looks like," said Daniel.

"Let's see, hey wait a minute, the Jumper still has Taonas in the computer!" Sheppard said. A display showing the outpost appeared on the window. "We should be approaching it... now." Sure enough, the rock dome of the outpost soon loomed into view.

O'Neill thought about asking why it was a rock dome, but changed his mind. He didn't want to know.

"Okay everyone, put on your suits. Tanner, stay with Sheppard in the jumper."

"Now how are we supposed to get in?"

"Easy, sir," said Sheppard. He fired a drone into the rock, making a sizable hole. "We land inside."

* * *

"This seemed quicker last time," said Carter through the radio.

"Probably because we had someone who was pretty much an Ancient," replied Daniel.

"Okay sir, you need to think of retriving the ZPM," Carter said to O'Neill.

"Remind me why _I_ have to do it?"

"Because you left Sheppard in the Jumper, sir."

After five minutes of inturrupted thoughts, O'Neill finally managed to retrieve the ZPM.

"This would go well with my coffee table," he joked as he placed it in a bag.

"We should get out of here before the dome collapses," urged Daniel.

"WHAT?!"

"Don't worry, I don't think it'll go-" a shake in the ground nearly knocked Mitchell off balance, "that quickly." His statement was followed by a quick, but well organized dash to the Jumper.

Sheppard sealed the door and took off. The dome collapsed mere seconds after they had cleared it.

"That was close," commented Mitchell, removing his hood.

"Too close, " said O'Neill, who had already removed his. "Well, time to go home,"

The jumper sped toward P5X-186, drive pods extended.

* * *

P5X-186 is not, and is not meant to be, a canon planet. I made up the number based on the CPU in my computer. A Core 2 Duo, which is the successor of the P4, hence P5. X is part of all the codes. The 186 comes from the clock speed, 1.86 GHz. I know you probably don't care, but I thought I'd put it in.

As always, please leave a review! I really like reviews!


	4. A New Life

Sorry that this chapter is so short. I tend to make chapter breaks based on events, not length.

"WHAT?! We don't get to go back to Atlantis?!"

"No, you are to stay clear of the Stargate program. Since there is already a... _Major_ John Sheppard, you are to assume a new identity."

* * *

"As the position you formerly occupied is occupied by a Doctor Weir, you will not return to it. In fact, you may not pursue a career in international relations, politics..."

* * *

"WHAT?! What do you mean I can't go back to Canada? I DEMAND to see the ambassador!"

"I advise you to calm down. You are to stay within a designated zone within the United States, and not leave it without permission..."

* * *

"We will turn you over to the government of the United Kingdom, but don't... expect the best of treatment."

* * *

"Unlike the others, you will go back to the Pegasus galaxy, where you will be turned over to your people... the Athosians."

* * *

"What are you gonna do with me? I'm not from here, and my planet's gone."

"Oh, I don't think you want to know..."

Ronon finally decided he had enough with this jerk. He slammed his fist into his face, killing him instantly. He pulled the gun from the man's belt, smashed the window, and jumped out of the car. Back to being a Runner, this time from someone else.

* * *

"What do you mean 'what do I have to do with it?' He did it on his own!"

"He is armed and extremely dangerous. What can you tell me about him?"

"Not much, I've only seen the guy once!"

* * *

"I don't think you'll ever see him again."

"Oh we will catch him, don't worry about that."

* * *

Running on Earth was a bit different to Ronon. Actually, it was a lot different. He quickly found out that beating the living daylights out of everyone in his path didn't work at all. Hiding required thinking, faking, and socializing, none of which he was good at. In fact, his 'hit everything' attitude almost got him caught.

_"You're that man, right? Don't hurt me, I won't tell?"_

_"Sure you won't," He hit him, but missed and hit his shoulder._

_"AAAAAAAAAAAAAAAAAAAAAAAAAAAH! SOMEONE CALL THE COPS! HELP!"_

_Ronon began running. He crashed through the door and scrambled down the flight of stairs. He stopped briefly at his room, grabbing a backpack prepared for this type of emergency and left, tossing a match into his garbage can._

_Hearing sirens, he hurried out the back door._

* * *

_One Month Later_

John woke up to the phone ringing.

"Hello,"

"It's about Ronon. They've caught him."

"You can't just put him in jail!"

"Oh yes we can. Assault, obstruction of justice, and..."

"What?"

"Tax fraud."

"Tax fraud?"

"Yes, tax fraud. In any case, he will be locked up in a secure facility for a very long time."

"Cut him some slack, will ya, he's from another planet."

"Oh yes about that. If he breathes a word to anyone he'll be transferred to a mental institution."

"And don't try anything, Sheppard. If you do, you'll be welcome to join him."

News spread to the other former Atlantis personell very quickly, and spread through SG-1 even faster.

* * *

_I'm sorry, but there's nothing we can do now. Any action on our part will lead to consequences of unknown severity._

_Come on, there must be something we can do!_

_Nope, we have no way of helping him. I'm sorry Sheppard._ Mitchell corrected it. _I'm sorry, Joe._

* * *

_Eleven Months Later_

Rodney woke up suddenly. His phone was ringing.

"Damn, I really gotta do something about that." He picked it up.

"This is Sam. The Goa'uld are coming. You'll get another call-" She was cut off when the second, higher priority, government call came through.

"Doctor McKay, you have thirty minutes to pack. A car is on the way. It's about the Stargate."

This story is focusing on Sheppard more and more. I don't know why- I think his position puts him near the center of the plot. This chapter was mostly talking, sorry about that, but I'll get to the action soon!


End file.
